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Harris BT, Rajasekaran V, Blackmur JP, O'Callaghan A, Donnelly K, Timofeeva M, Vaughan-Shaw PG, Din FVN, Dunlop MG, Farrington SM. Transcriptional dynamics of colorectal cancer risk associated variation at 11q23.1 correlate with tuft cell abundance and marker expression in silico. Sci Rep 2022; 12:13609. [PMID: 35948568 PMCID: PMC9365857 DOI: 10.1038/s41598-022-17887-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
Colorectal cancer (CRC) is characterised by heritable risk that is not well understood. Heritable, genetic variation at 11q23.1 is associated with increased colorectal cancer (CRC) risk, demonstrating eQTL effects on 3 cis- and 23 trans-eQTL targets. We sought to determine the relationship between 11q23.1 cis- and trans-eQTL target expression and test for potential cell-specificity. scRNAseq from 32,361 healthy colonic epithelial cells was aggregated and subject to weighted gene co-expression network analysis (WGCNA). One module (blue) included 19 trans-eQTL targets and was correlated with POU2AF2 expression only. Following unsupervised clustering of single cells, the expression of 19 trans-eQTL targets was greatest and most variable in cluster number 11, which transcriptionally resembled tuft cells. 14 trans-eQTL targets were found to demarcate this cluster, 11 of which were corroborated in a second dataset. Intra-cluster WGCNA and module preservation analysis then identified twelve 11q23.1 trans-eQTL targets to comprise a network that was specific to cluster 11. Finally, linear modelling and differential abundance testing showed 11q23.1 trans-eQTL target expression was predictive of cluster 11 abundance. Our findings suggest 11q23.1 trans-eQTL targets comprise a POU2AF2-related network that is likely tuft cell-specific and reduced expression of these genes correlates with reduced tuft cell abundance in silico.
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Affiliation(s)
- Bradley T Harris
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Vidya Rajasekaran
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James P Blackmur
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Alan O'Callaghan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maria Timofeeva
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Public Health, D-IAS, Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Peter G Vaughan-Shaw
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Farhat V N Din
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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2
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Ali MW, Chen J, Yan L, Wang X, Dai JY, Vaughan TL, Casey G, Buas MF. A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets. Hum Mol Genet 2022; 31:3975-3986. [PMID: 35766871 DOI: 10.1093/hmg/ddac141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/12/2022] Open
Abstract
Nineteen genetic susceptibility loci for esophageal adenocarcinoma (EAC) and its precursor Barrett's esophagus (BE) have been identified through genome-wide association studies (GWAS). Clinical translation of such discoveries, however, has been hindered by the slow pace of discovery of functional/causal variants and gene targets at these loci. We previously developed a systematic informatics pipeline to prioritize candidate functional variants using functional potential scores, applied the pipeline to select high-scoring BE/EAC risk loci, and validated a functional variant at chr19p13.11 (rs10423674). Here, we selected two additional prioritized loci for experimental interrogation: chr3p13/rs1522552 and chr8p23.1/rs55896564. Candidate enhancer regions encompassing these variants were evaluated using luciferase reporter assays in two EAC cell lines. One of the two regions tested exhibited allele-specific enhancer activity - 8p23.1/rs55896564. CRISPR-mediated deletion of the putative enhancer in EAC cell lines correlated with reduced expression of three candidate gene targets: B lymphocyte kinase (BLK), nei like DNA glycosylase 2 (NEIL2), and cathepsin B (CTSB). Expression quantitative trait locus (eQTL) mapping in normal esophagus and stomach revealed strong associations between the BE/EAC risk allele at rs55896564 (G) and lower expression of CTSB, a protease gene implicated in epithelial wound repair. These results further support the utility of functional potential scores for GWAS variant prioritization, and provide the first experimental evidence of a functional variant and risk enhancer at the 8p23.1 GWAS locus. Identification of CTSB, BLK, and NEIL2 as candidate gene targets suggests that altered expression of these genes may underlie the genetic risk association at 8p23.1 with BE/EAC.
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Affiliation(s)
- Mourad Wagdy Ali
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Jianhong Chen
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiaoyu Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James Y Dai
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas L Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Epidemiology, University of Washington, School of Public Health, Seattle, Washington, USA
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Matthew F Buas
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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Fu J, Qin W, Tong Q, Li Z, Shao Y, Liu Z, Liu C, Wang Z, Xu X. A novel DNA methylation-driver gene signature for long-term survival prediction of hepatitis-positive hepatocellular carcinoma patients. Cancer Med 2022; 11:4721-4735. [PMID: 35637633 PMCID: PMC9741990 DOI: 10.1002/cam4.4838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Abnormal DNA methylation is one of the most general epigenetic modifications in hepatocellular carcinoma (HCC). Recent research showed that DNA methylation was a prognostic indicator of all-cause HCC and nonviral HCC. However, whether DNA methylation-driver genes could be used for predicting survival, the probability of hepatitis-positive HCC remains unclear. METHODS In this study, DNA methylation-driver genes (MDGs) were screened by a joint analysis of methylome and transcriptome data of 142 hepatitis-positive HCC patients. Subsequently, a prognostic risk score and nomogram were constructed. Finally, correlation analyses between the risk score and signaling pathways and immunity were conducted by GSVA and CIBERSORT. RESULTS Through random forest screening and Cox progression analysis, 10 prognostic methylation-driver genes (AC008271.1, C11orf53, CASP8, F2RL2, GBP5, LUCAT1, RP11-114B7.6, RP11-149I23.3, RP11-383 J24.1, and SLC35G2) were screened out. As a result, a prognostic risk score signature was constructed. The independent value of the risk score for prognosis prediction were addressed in the TCGA-HCC and the China-HCC cohorts. Next, clinicopathological features were analyzed and HBV status and histological grade were screened to construct a nomogram together with the risk score. The prognostic efficiency of the nomogram was validated by the calibration curves and the concordance index (C index: 0.829, 95% confidence interval: 0.794-0.864), while its clinical application ability was confirmed by decision curve analysis (DCA). At last, the relationship between the risk score and signaling pathways, as well as the correlations between immune cells were elucidated preliminary. CONCLUSIONS Taken together, our study explored a novel DNA methylation-driver gene risk score signature and an efficient nomogram for long-term survival prediction of hepatitis-positive HCC patients.
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Affiliation(s)
- Jie Fu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Wei Qin
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Qing Tong
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhenghao Li
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yaoli Shao
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiqiang Liu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Chun Liu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zicheng Wang
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xundi Xu
- Department of General SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgerySouth China Hospital of Shenzhen UniversityShenzhenChina
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4
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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5
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Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids. Oncotarget 2021; 12:1863-1877. [PMID: 34548904 PMCID: PMC8448508 DOI: 10.18632/oncotarget.28058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/13/2021] [Indexed: 12/23/2022] Open
Abstract
Tobacco smoke and red/processed meats are well-known risk factors for colorectal cancer (CRC). Most research has focused on studies of normal colon biopsies in epidemiologic studies or treatment of CRC cell lines in vitro. These studies are often constrained by challenges with accuracy of self-report data or, in the case of CRC cell lines, small sample sizes and lack of relationship to normal tissue at risk. In an attempt to address some of these limitations, we performed a 24-hour treatment of a representative carcinogens cocktail in 37 independent organoid lines derived from normal colon biopsies. Machine learning algorithms were applied to bulk RNA-sequencing and revealed cellular composition changes in colon organoids. We identified 738 differentially expressed genes in response to carcinogens exposure. Network analysis identified significantly different modules of co-expression, that included genes related to MSI-H tumor biology, and genes previously implicated in CRC through genome-wide association studies. Our study helps to better define the molecular effects of representative carcinogens from smoking and red/processed meat in normal colon epithelial cells and in the etiology of the MSI-H subtype of CRC, and suggests an overlap between molecular mechanisms involved in inherited and environmental CRC risk.
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Chen J, Ali MW, Yan L, Dighe SG, Dai JY, Vaughan TL, Casey G, Buas MF. Prioritization and functional analysis of GWAS risk loci for Barrett's esophagus and esophageal adenocarcinoma. Hum Mol Genet 2021; 31:410-422. [PMID: 34505128 DOI: 10.1093/hmg/ddab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/17/2021] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified ~ 20 genetic susceptibility loci for esophageal adenocarcinoma (EAC), and its precursor, Barrett's esophagus (BE). Despite such advances, functional/causal variants and gene targets at these loci remain undefined, hindering clinical translation. A key challenge is that most causal variants map to non-coding regulatory regions such as enhancers, and typically, numerous potential candidate variants at GWAS loci require testing. We developed a systematic informatics pipeline for prioritizing candidate functional variants via integrative functional potential scores consolidated from multi-omics annotations, and used this pipeline to identify two high-scoring variants for experimental interrogation: chr9q22.32/rs11789015 and chr19p13.11/rs10423674. Minimal candidate enhancer regions spanning these variants were evaluated using luciferase reporter assays in two EAC cell lines. One of the two variants tested (rs10423674) exhibited allele-specific enhancer activity. CRISPR-mediated deletion of the putative enhancer region in EAC cell lines correlated with reduced expression of two genes-CREB-regulated transcription coactivator 1 (CRTC1) and Cartilage oligomeric matrix protein (COMP); expression of five other genes remained unchanged (CRLF1, KLHL26, TMEM59L, UBA52, RFXANK). Expression quantitative trait locus (eQTL) mapping indicated that rs10423674 genotype correlated with CRTC1 and COMP expression in normal esophagus. This study represents the first experimental effort to bridge GWAS associations to biology in BE/EAC, and supports the utility of functional potential scores to guide variant prioritization. Our findings reveal a functional variant and candidate risk enhancer at chr19p13.11, and implicate CRTC1 and COMP as putative gene targets, suggesting that altered expression of these genes may underlie the BE/EAC risk association.
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Affiliation(s)
- Jianhong Chen
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263 USA
| | - Mourad Wagdy Ali
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22903 USA
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263 USA
| | - Shruti G Dighe
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263 USA
| | - James Y Dai
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109 USA
| | - Thomas L Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109 USA.,Department of Epidemiology, University of Washington, School of Public Health, Seattle, Washington, 98195 USA
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22903 USA
| | - Matthew F Buas
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263 USA
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7
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Mur P, Bonifaci N, Díez-Villanueva A, Munté E, Alonso MH, Obón-Santacana M, Aiza G, Navarro M, Piñol V, Brunet J, Tomlinson I, Capellá G, Moreno V, Valle L. Non-Lynch Familial and Early-Onset Colorectal Cancer Explained by Accumulation of Low-Risk Genetic Variants. Cancers (Basel) 2021; 13:3857. [PMID: 34359758 PMCID: PMC8345397 DOI: 10.3390/cancers13153857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 01/07/2023] Open
Abstract
A large proportion of familial and/or early-onset cancer patients do not carry pathogenic variants in known cancer predisposing genes. We aimed to assess the contribution of previously validated low-risk colorectal cancer (CRC) alleles to familial/early-onset CRC (fCRC) and to serrated polyposis. We estimated the association of CRC with a 92-variant-based weighted polygenic risk score (wPRS) using 417 fCRC patients, 80 serrated polyposis patients, 1077 hospital-based incident CRC patients, and 1642 controls. The mean wPRS was significantly higher in fCRC than in controls or sporadic CRC patients. fCRC patients in the highest (20th) wPRS quantile were at four-fold greater CRC risk than those in the middle quantile (10th). Compared to low-wPRS fCRC, a higher number of high-wPRS fCRC patients had developed multiple primary CRCs, had CRC family history, and were diagnosed at age ≥50. No association with wPRS was observed for serrated polyposis. In conclusion, a relevant proportion of mismatch repair (MMR)-proficient fCRC cases might be explained by the accumulation of low-risk CRC alleles. Validation in independent cohorts and development of predictive models that include polygenic risk score (PRS) data and other CRC predisposing factors will determine the implementation of PRS into genetic testing and counselling in familial and early-onset CRC.
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Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Nuria Bonifaci
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
| | - Anna Díez-Villanueva
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Elisabet Munté
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
| | - Maria Henar Alonso
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Mireia Obón-Santacana
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Virginia Piñol
- Gastroenterology Unit, Hospital Universitario de Girona Dr Josep Trueta, 17007 Girona, Spain;
- School of Medicine, University of Girona, 17071 Girona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
- School of Medicine, University of Girona, 17071 Girona, Spain
- Catalan Institute of Oncology, IDIBGi, 17007 Girona, Spain
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh EH4 2XR, UK;
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Victor Moreno
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, IDIBELL, 08908 Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029 Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, 08908 Barcelona, Spain; (P.M.); (N.B.); (E.M.); (G.A.); (M.N.); (J.B.); (G.C.)
- Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Spain; (A.D.-V.); (M.H.A.); (M.O.-S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029 Madrid, Spain
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8
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Ali MW, Patro CPK, Devall M, Dampier CH, Plummer SJ, Kuscu C, Adli M, Lai RK, Casey G. A Functional Variant on 9p21.3 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1. Hum Mutat 2021; 42:1208-1214. [PMID: 34153138 PMCID: PMC8519084 DOI: 10.1002/humu.24244] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/12/2021] [Accepted: 06/13/2021] [Indexed: 12/13/2022]
Abstract
Genome‐wide association studies have identified SNPs associated with glioma risk on 9p21.3, but biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 9p21.3 affects activity of an enhancer, causing altered expression of nearby genes. We considered all SNPs in linkage disequilibrium with the 9p21.3 sentinel SNP rs634537 that mapped to putative enhancers. An enhancer containing rs1537372 exhibited allele‐specific effects on luciferase activity. Deletion of this enhancer in GBM cell lines correlated with decreased expression of CDKN2B‐AS1. Expression quantitative trait loci analysis using non‐diseased brain samples showed rs1537372 to be a consistently significant eQTL for CDKN2B‐AS1. Additionally, our analysis of Hi‐C data generated in neural progenitor cells showed that the bait region containing rs1537372 interacted with the CDKN2B‐AS1 promoter. These data suggest rs1537372, a SNP at the 9p21.3 risk locus, is a functional variant that modulates expression of CDKN2B‐AS1.
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Affiliation(s)
- Mourad Wagdy Ali
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908
| | - C Pawan K Patro
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033
| | - Matthew Devall
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908
| | - Christopher H Dampier
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908
| | - Sarah J Plummer
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908
| | - Cem Kuscu
- Department of Surgery, James D. Eason Transplant Research Institute, University of Tennessee, Memphis, TN, 38163
| | - Mazhar Adli
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, 60611
| | - Rose K Lai
- Departments of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033
| | - Graham Casey
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908
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9
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Patro CPK, Nousome D, Lai RK. Meta-Analyses of Splicing and Expression Quantitative Trait Loci Identified Susceptibility Genes of Glioma. Front Genet 2021; 12:609657. [PMID: 33936159 PMCID: PMC8081720 DOI: 10.3389/fgene.2021.609657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background The functions of most glioma risk alleles are unknown. Very few studies had evaluated expression quantitative trait loci (eQTL), and insights of susceptibility genes were limited due to scarcity of available brain tissues. Moreover, no prior study had examined the effect of glioma risk alleles on alternative RNA splicing. Objective This study explored splicing quantitative trait loci (sQTL) as molecular QTL and improved the power of QTL mapping through meta-analyses of both cis eQTL and sQTL. Methods We first evaluated eQTLs and sQTLs of the CommonMind Consortium (CMC) and Genotype-Tissue Expression Project (GTEx) using genotyping, or whole-genome sequencing and RNA-seq data. Alternative splicing events were characterized using an annotation-free method that detected intron excision events. Then, we conducted meta-analyses by pooling the eQTL and sQTL results of CMC and GTEx using the inverse variance-weighted model. Afterward, we integrated QTL meta-analysis results (Q < 0.05) with the Glioma International Case Control Study (GICC) GWAS meta-analysis (case:12,496, control:18,190), using a summary statistics-based mendelian randomization (SMR) method. Results Between CMC and GTEx, we combined the QTL data of 354 unique individuals of European ancestry. SMR analyses revealed 15 eQTLs in 11 loci and 32 sQTLs in 9 loci relevant to glioma risk. Two loci only harbored sQTLs (1q44 and 16p13.3). In seven loci, both eQTL and sQTL coexisted (2q33.3, 7p11.2, 11q23.3 15q24.2, 16p12.1, 20q13.33, and 22q13.1), but the target genes were different for five of these seven loci. Three eQTL loci (9p21.3, 20q13.33, and 22q13.1) and 4 sQTL loci (11q23.3, 16p13.3, 16q12.1, and 20q13.33) harbored multiple target genes. Eight target genes of sQTLs (C2orf80, SEC61G, TMEM25, PHLDB1, RP11-161M6.2, HEATR3, RTEL1-TNFRSF6B, and LIME1) had multiple alternatively spliced transcripts. Conclusion Our study revealed that the regulation of transcriptome by glioma risk alleles is complex, with the potential for eQTL and sQTL jointly affecting gliomagenesis in risk loci. QTLs of many loci involved multiple target genes, some of which were specific to alternative splicing. Therefore, quantitative trait loci that evaluate only total gene expression will miss many important target genes.
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Affiliation(s)
- C Pawan K Patro
- Department of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, United States
| | - Darryl Nousome
- Center for Prostate Disease Research, Department of Surgery, Uniformed Services University of the Health Sciences, Rockville, MD, United States
| | | | - Rose K Lai
- Department of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA, United States
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10
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Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle ADL, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W. Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. Gastroenterology 2021; 160:1164-1178.e6. [PMID: 33058866 PMCID: PMC7956223 DOI: 10.1053/j.gastro.2020.08.062] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND AND AIMS Susceptibility genes and the underlying mechanisms for the majority of risk loci identified by genome-wide association studies (GWAS) for colorectal cancer (CRC) risk remain largely unknown. We conducted a transcriptome-wide association study (TWAS) to identify putative susceptibility genes. METHODS Gene-expression prediction models were built using transcriptome and genetic data from the 284 normal transverse colon tissues of European descendants from the Genotype-Tissue Expression (GTEx), and model performance was evaluated using data from The Cancer Genome Atlas (n = 355). We applied the gene-expression prediction models and GWAS data to evaluate associations of genetically predicted gene-expression with CRC risk in 58,131 CRC cases and 67,347 controls of European ancestry. Dual-luciferase reporter assays and knockdown experiments in CRC cells and tumor xenografts were conducted. RESULTS We identified 25 genes associated with CRC risk at a Bonferroni-corrected threshold of P < 9.1 × 10-6, including genes in 4 novel loci, PYGL (14q22.1), RPL28 (19q13.42), CAPN12 (19q13.2), MYH7B (20q11.22), and MAP1L3CA (20q11.22). In 9 known GWAS-identified loci, we uncovered 9 genes that have not been reported previously, whereas 4 genes remained statistically significant after adjusting for the lead risk variant of the locus. Through colocalization analysis in GWAS loci, we additionally identified 12 putative susceptibility genes that were supported by TWAS analysis at P < .01. We showed that risk allele of the lead risk variant rs1741640 affected the promoter activity of CABLES2. Knockdown experiments confirmed that CABLES2 plays a vital role in colorectal carcinogenesis. CONCLUSIONS Our study reveals new putative susceptibility genes and provides new insight into the biological mechanisms underlying CRC development.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Weiqiang Lin
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeroen Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephanie Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Tabitha Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yuan Yuan
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangqin Wang
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengqiu Bai
- The Kidney Disease Center, the First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Goncalo R Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire, Nantes, France
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, United Kingdom
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | | | - Peter T Campbell
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany; University Medical Centre Hamburg-Eppendorf, University Cancer Centre Hamburg, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sang Hee Cho
- Department of Hematology-Oncology, Chonnam National University Hospital, Hwasun, South Korea
| | - David V Conti
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics and the Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Edith J M Feskens
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Steven J Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Mark Guinter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Marc J Gunter
- Nutrition and Metabolism Section, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden, Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Ellen Kampman
- Division of Human Nutrition and Health, Wageningen University and Research, Wageningen, the Netherlands
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina
| | - Hyeong Rok Kim
- Department of Surgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | | | - Soo Chin Lee
- National University Cancer Institute, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Neil Murphy
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; School of Public Health, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Rachel Pearlman
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Paul D P Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth A Platz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Lady Davis Carmel Medical Center, Haifa, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lori C Sakoda
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Division of Research, Kaiser Permanente Northern California, Oakland, California
| | - Clemens Schafmayer
- Department of General Surgery, University Hospital Rostock, Rostock, Germany
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | | | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic; Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Xiaoliang Wang
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Michael O Woods
- Memorial University of Newfoundland, Discipline of Genetics, St John's, Newfoundland and Labrador, Canada
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen B Gruber
- Department of Preventive Medicine and University of Southern California Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington; Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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11
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Fortini BK, Tring S, Devall MA, Ali MW, Plummer SJ, Casey G. SNPs associated with colorectal cancer at 15q13.3 affect risk enhancers that modulate GREM1 gene expression. Hum Mutat 2021; 42:237-245. [PMID: 33476087 PMCID: PMC7898835 DOI: 10.1002/humu.24166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 08/12/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Several genome wide association studies of colorectal cancer (CRC) have identified single nucleotide polymorphisms (SNPs) on chromosome 15q13.3 associated with CRC risk. To identify functional variant(s) underlying this association, we investigated SNPs in linkage disequilibrium with the risk‐associated SNP rs4779584 that overlapped regulatory regions/enhancer elements characterized in colon‐related tissues and cells. We identified several SNP‐containing regulatory regions that exhibited enhancer activity in vitro, including one SNP (rs1406389) that correlated with allele‐specific effects on enhancer activity. Deletion of either this enhancer or another enhancer that had previously been reported in this region correlated with decreased expression of GREM1 following CRISPR/Cas9 genome editing. That GREM1 is one target of these enhancers was further supported by an expression quantitative trait loci correlation between rs1406389 and GREM1 expression in the transverse but not sigmoid colon in the Genotype‐Tissue Expression dataset. Taken together, we conclude that the 15q13.3 region contains at least two functional variants that map to distinct enhancers and impact CRC risk through modulation of GREM1 expression.
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Affiliation(s)
| | - Stephanie Tring
- Molecular Genomics Core, University of Southern California, Los Angeles, California, USA
| | - Matthew A Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Mourad Wagdy Ali
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Sarah J Plummer
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
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12
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Ali MW, Patro CPK, Zhu JJ, Dampier CH, Plummer SJ, Kuscu C, Adli M, Lau C, Lai RK, Casey G. A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes. Hum Mutat 2020; 42:77-88. [PMID: 33169458 PMCID: PMC7839675 DOI: 10.1002/humu.24134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022]
Abstract
Genome‐wide association studies (GWAS) have identified single‐nucleotide polymorphisms (SNPs) associated with glioma risk on 20q13.33, but the biological mechanisms underlying this association are unknown. We tested the hypothesis that a functional SNP on 20q13.33 impacted the activity of an enhancer, leading to an altered expression of nearby genes. To identify candidate functional SNPs, we identified all SNPs in linkage disequilibrium with the risk‐associated SNP rs2297440 that mapped to putative enhancers. Putative enhancers containing candidate functional SNPs were tested for allele‐specific effects in luciferase enhancer activity assays against glioblastoma multiforme (GBM) cell lines. An enhancer containing SNP rs3761124 exhibited allele‐specific effects on activity. Deletion of this enhancer by CRISPR‐Cas9 editing in GBM cell lines correlated with an altered expression of multiple genes, including STMN3, RTEL1, RTEL1‐TNFRSF6B, GMEB2, and SRMS. Expression quantitative trait loci (eQTL) analyses using nondiseased brain samples, isocitrate dehydrogenase 1 (IDH1) wild‐type glioma, and neurodevelopmental tissues showed STMN3 to be a consistent significant eQTL with rs3761124. RTEL1 and GMEB2 were also significant eQTLs in the context of early CNS development and/or in IDH1 wild‐type glioma. We provide evidence that rs3761124 is a functional variant on 20q13.33 related to glioma/GBM risk that modulates the expression of STMN3 and potentially other genes across diverse cellular contexts.
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Affiliation(s)
- Mourad Wagdy Ali
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - C Pawan K Patro
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Christopher H Dampier
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Sarah J Plummer
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Cem Kuscu
- Department of Surgery, James D. Eason Transplant Research Institute, University of Tennessee, Memphis, Tennessee, USA
| | - Mazhar Adli
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, Illinois, USA
| | - Ching Lau
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Rose K Lai
- Departments of Neurology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Graham Casey
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
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13
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Bien SA, Su YR, Conti DV, Harrison TA, Qu C, Guo X, Lu Y, Albanes D, Auer PL, Banbury BL, Berndt SI, Bézieau S, Brenner H, Buchanan DD, Caan BJ, Campbell PT, Carlson CS, Chan AT, Chang-Claude J, Chen S, Connolly CM, Easton DF, Feskens EJM, Gallinger S, Giles GG, Gunter MJ, Hampe J, Huyghe JR, Hoffmeister M, Hudson TJ, Jacobs EJ, Jenkins MA, Kampman E, Kang HM, Kühn T, Küry S, Lejbkowicz F, Le Marchand L, Milne RL, Li L, Li CI, Lindblom A, Lindor NM, Martín V, McNeil CE, Melas M, Moreno V, Newcomb PA, Offit K, Pharaoh PDP, Potter JD, Qu C, Riboli E, Rennert G, Sala N, Schafmayer C, Scacheri PC, Schmit SL, Severi G, Slattery ML, Smith JD, Trichopoulou A, Tumino R, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Weinstein SJ, White E, Wolk A, Woods MO, Wu AH, Abecasis GR, Casey G, Nickerson DA, Gruber SB, Hsu L, Zheng W, Peters U. Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer. Hum Genet 2019; 138:307-326. [PMID: 30820706 PMCID: PMC6483948 DOI: 10.1007/s00439-019-01989-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 02/02/2023]
Abstract
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10- 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10- 4, replication P = 6.7 × 10- 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
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Affiliation(s)
- Stephanie A Bien
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
| | - Yu-Ru Su
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David V Conti
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tabitha A Harrison
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Conghui Qu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Xingyi Guo
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Yingchang Lu
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, 53205, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Barbara L Banbury
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stéphane Bézieau
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Colorectal Oncogenomics Group, Department of Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
- Genetic Medicine and Familial Cancer Centre, The Royal Melbourne Hospital, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, 94612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Genetic Tumour Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, 20246, Hamburg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sai Chen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Charles M Connolly
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care School of Clinical Medicine, University of Cambridge, Cambridge, England, 01223, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Edith J M Feskens
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, 1X5, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marc J Gunter
- Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, 01307, Dresden, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeroen R Huyghe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- AbbVie Inc, 1500 Seaport Blvd, Redwood City, CA, 94063, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Eric J Jacobs
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, 30329-4251, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Ellen Kampman
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Tilman Kühn
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Sébastien Küry
- Centre Hospitalier Universitaire Hotel-Dieu, 44093, Nantes, France
- Service de Génétique Médiczle, Centre Hospitalier Universitaire (CHU), 44093, Nantes, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Flavio Lejbkowicz
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Loic Le Marchand
- University of Hawai'i Cancer Center, Honolulu, Hawaii, 96813, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, 3010, Australia
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, 3004, Australia
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Li
- Department of Family Medicine and Community Health, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Annika Lindblom
- Department of Clinical Genetics, Karolinska University Hospital Solna, 171 77, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet Solna, 171 77, Stockholm, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, AZ, 85259, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Vicente Martín
- Biomedicine Institute (IBIOMED), University of León, León, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Caroline E McNeil
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Marilena Melas
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Victor Moreno
- CIBER Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), 08028, Barcelona, Spain
- University of Barcelona, 08007, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Polly A Newcomb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Kenneth Offit
- Department of Medicine, Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Paul D P Pharaoh
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, CB2 1TN, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - John D Potter
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Chenxu Qu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gad Rennert
- Clalit Health Services National Israeli Cancer Control Center, 34361, Haifa, Israel
- Department of Community Medicine and Epidemiology, Carmel Medical Center, 34361, Haifa, Israel
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Molecular Epidemiology Group, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Campus Kiel, 24118, Kiel, Germany
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, Inc, Tampa, FL, 33612, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gianluca Severi
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Joshua D Smith
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Antonia Trichopoulou
- Hellenic Health Foundation, 13 Kaisareias & Alexandroupoleos, 115 27, Athens, Greece
- WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Mikras Asias 75, 115 27, Athens, Greece
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Rosario Tumino
- Affiliation Cancer Registry, Department of Prevention, Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Cornelia M Ulrich
- Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Fränzel J B van Duijnhoven
- Division of Human Nutrition, Wageningen University & Research, Wageningen, The Netherlands
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Bethany Van Guelpen
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephanie J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20892, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet Solna, 17177, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, 75121, Uppsala, Sweden
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, Saint John's, NL, A1B 3V6, Canada
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Anna H Wu
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Goncalo R Abecasis
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Graham Casey
- Centre for Research in Epidemiology and Population Health, Institut de Cancérologie Gustave Roussy, Villejuif, France
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Deborah A Nickerson
- Department Genome Sciences, University of Washington, 98195, Seattle, WA, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Wei Zheng
- Division of Epidemiology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
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14
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Menor M, Zhu Y, Wang Y, Zhang J, Jiang B, Deng Y. Development of somatic mutation signatures for risk stratification and prognosis in lung and colorectal adenocarcinomas. BMC Med Genomics 2019; 12:24. [PMID: 30704450 PMCID: PMC6357362 DOI: 10.1186/s12920-018-0454-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Prognostic signatures are vital to precision medicine. However, development of somatic mutation prognostic signatures for cancers remains a challenge. In this study we developed a novel method for discovering somatic mutation based prognostic signatures. Results Somatic mutation and clinical data for lung adenocarcinoma (LUAD) and colorectal adenocarcinoma (COAD) from The Cancer Genome Atlas (TCGA) were randomly divided into training (n = 328 for LUAD and 286 for COAD) and validation (n = 167 for LUAD and 141 for COAD) datasets. A novel method of using the log2 ratio of the tumor mutation frequency to the paired normal mutation frequency is computed for each patient and missense mutation. The missense mutation ratios were mean aggregated into gene-level somatic mutation profiles. The somatic mutations were assessed using univariate Cox analysis on the LUAD and COAD training sets separately. Stepwise multivariate Cox analysis resulted in a final gene prognostic signature for LUAD and COAD. Performance was compared to gene prognostic signatures generated using the same pipeline but with different somatic mutation profile representations based on tumor mutation frequency, binary calls, and gene-gene network normalization. Signature high-risk LUAD and COAD cases had worse overall survival compared to the signature low-risk cases in the validation set (log-rank test p-value = 0.0101 for LUAD and 0.0314 for COAD) using mutation tumor frequency ratio (MFR) profiles, while all other methods, including gene-gene network normalization, have statistically insignificant stratification (log-rank test p-value ≥0.05). Most of the genes in the final gene signatures using MFR profiles are cancer-related based on network and literature analysis. Conclusions We demonstrated the robustness of MFR profiles and its potential to be a powerful prognostic tool in cancer. The results are robust according to validation testing and the selected genes are biologically relevant.
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Affiliation(s)
- Mark Menor
- Department of Complementary & Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Yong Zhu
- National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Yu Wang
- Department of Complementary & Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.,Department of Oncology, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210001, Jiangsu Province, China
| | - Jicai Zhang
- Department of Laboratory Medicine, Shiyan Taihe Hospital, College of Biomedical Engineering, Hubei University of Medicine, Shiyan, Hubei, 442000, People's Republic of China
| | - Bin Jiang
- National Medical Centre of Colorectal Disease, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.
| | - Youping Deng
- Department of Complementary & Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.
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15
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Ke J, Lou J, Chen X, Li J, Liu C, Gong Y, Yang Y, Zhu Y, Zhang Y, Tian J, Chang J, Zhong R, Gong J, Miao X. Identification of a functional variant for colorectal cancer risk mapping to chromosome 5q31.1. Oncotarget 2018; 7:35199-207. [PMID: 27177089 PMCID: PMC5085221 DOI: 10.18632/oncotarget.9298] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWASs) have established chromosome 5q31.1 as a risk locus for colorectal cancer (CRC). We previously identified a potentially regulatory single nucleotide polymorphism (SNP) rs17716310 within 5q31.1. Now, we extended our study with another independent Chinese population, functional assays and analyses of TCGA (The Cancer Genome Atlas) data. Significant associations between rs17716310 and CRC risk were found in Present Study including 1075 CRC cases and 1999 controls (additive model: OR = 1.149, 95% CI = 1.027–1.286, P = 0.016), and in Combined Study including 1766 cases and 2708 controls (additive model: OR = 1.145, 95% CI = 1.045–1.254, P = 0.004). Dual luciferase reporter gene assays indicated that the variant C allele obviously increased transcriptional activity. Using TCGA datasets, we indicated rs17716310 as a cis expression quantitative trait locus (eQTL) for the gene SMAD5, whose expression was significantly higher in CRC tissues. These findings suggested that the functional polymorphism rs17716310 A > C might be a genetic modifier for CRC, promoting the expression of SMAD5 that belonged to the transforming growth factor beta (TGF-β) signaling pathway.
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Affiliation(s)
- Juntao Ke
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueqin Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Ghorbanoghli Z, Nieuwenhuis MH, Houwing-Duistermaat JJ, Jagmohan-Changur S, Hes FJ, Tops CM, Wagner A, Aalfs CM, Verhoef S, Gómez García EB, Sijmons RH, Menko FH, Letteboer TG, Hoogerbrugge N, van Wezel T, Vasen HFA, Wijnen JT. Colorectal cancer risk variants at 8q23.3 and 11q23.1 are associated with disease phenotype in APC mutation carriers. Fam Cancer 2017; 15:563-70. [PMID: 26880076 PMCID: PMC5010832 DOI: 10.1007/s10689-016-9877-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Familial adenomatous polyposis (FAP) is a dominantly inherited syndrome caused by germline mutations in the APC gene and characterized by the development of multiple colorectal adenomas and a high risk of developing colorectal cancer (CRC). The severity of polyposis is correlated with the site of the APC mutation. However, there is also phenotypic variability within families with the same underlying APC mutation, suggesting that additional factors influence the severity of polyposis. Genome-wide association studies identified several single nucleotide polymorphisms (SNPs) that are associated with CRC. We assessed whether these SNPs are associated with polyp multiplicity in proven APC mutation carriers. Sixteen CRC-associated SNPs were analysed in a cohort of 419 APC germline mutation carriers from 182 families. Clinical data were retrieved from the Dutch Polyposis Registry. Allele frequencies of the SNPs were compared for patients with <100 colorectal adenomas versus patients with ≥100 adenomas, using generalized estimating equations with the APC genotype as a covariate. We found a trend of association of two of the tested SNPs with the ≥100 adenoma phenotype: the C alleles of rs16892766 at 8q23.3 (OR 1.71, 95 % CI 1.05-2.76, p = 0.03, dominant model) and rs3802842 at 11q23.1 (OR 1.51, 95 % CI 1.03-2.22, p = 0.04, dominant model). We identified two risk variants that are associated with a more severe phenotype in APC mutation carriers. These risk variants may partly explain the phenotypic variability in families with the same APC gene defect. Further studies with a larger sample size are recommended to evaluate and confirm the phenotypic effect of these SNPs in FAP.
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Affiliation(s)
- Z Ghorbanoghli
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands.
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA, Leiden, The Netherlands.
| | - M H Nieuwenhuis
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands
| | - J J Houwing-Duistermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - S Jagmohan-Changur
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - F J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Wagner
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - C M Aalfs
- Department of Clinical Genetics, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - S Verhoef
- Family Cancer Clinic, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E B Gómez García
- Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands
| | - R H Sijmons
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - F H Menko
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - T G Letteboer
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - T van Wezel
- Departments of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - H F A Vasen
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA, Leiden, The Netherlands
| | - J T Wijnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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17
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Loo LWM, Lemire M, Le Marchand L. In silico pathway analysis and tissue specific cis-eQTL for colorectal cancer GWAS risk variants. BMC Genomics 2017; 18:381. [PMID: 28506205 PMCID: PMC5432975 DOI: 10.1186/s12864-017-3750-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 05/02/2017] [Indexed: 02/08/2023] Open
Abstract
Background Genome-wide association studies have identified 55 genetic variants associated with colorectal cancer risk to date. However, potential causal genes and pathways regulated by these risk variants remain to be characterized. Therefore, we performed gene ontology enrichment and pathway analyses to determine if there was an enrichment of genes in proximity to the colorectal cancer risk variants that could further elucidate the probable causal genes and pathways involved in colorectal cancer biology. Results For the 65 unique genes that either contained, or were immediately neighboring up- and downstream, of these variants there was a significant enrichment for the KEGG pathway, Pathways in Cancer (p-value = 2.67 × 10−5) and an enrichment for multiple biological processes (FDR < 0.05), such as cell junction organization, tissue morphogenesis, regulation of SMAD protein phosphorylation, and odontogenesis identified through Gene Ontology analysis. To identify potential causal genes, we conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using gene expression and genotype data from the Genotype-Tissue Expression (GTEx) Project portal in normal sigmoid (n = 124) and transverse (n = 169) colon tissue. In addition, we also did a cis-eQTL analysis on colorectal tumor tissue (n = 147) from The Cancer Genome Atlas (TCGA). We identified two risk alleles that were significant cis-eQTLs for FADS2 (rs1535) and COLCA1 and 2 (rs3802842) genes in the normal transverse colon tissue and two risk alleles that were significant cis-eQTLs for the CABLES2 (rs2427308) and LIPG (rs7229639) genes in the normal sigmoid colon tissue, but not tumor tissue. Conclusions Our data reaffirm the potential to identify an enrichment for biological processes and candidate causal genes based on expression profiles correlated with genetic risk alleles of colorectal cancer, however, the identification of these significant cis-eQTLs is context and tissue specific. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3750-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lenora W M Loo
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA.
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Loïc Le Marchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
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18
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Zhai K, Chang J, Hu J, Wu C, Lin D. Germline variation in the 3'-untranslated region of the POU2AF1 gene is associated with susceptibility to lymphoma. Mol Carcinog 2017; 56:1945-1952. [PMID: 28345816 DOI: 10.1002/mc.22652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 03/05/2017] [Accepted: 03/23/2017] [Indexed: 01/06/2023]
Abstract
Genetic variations in certain genes may alter the susceptibility to lymphoma. We searched electronic databases and selected candidate single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect miRNA-binding ability in the 50 most dysregulated genes in lymphoma for further study. We found that rs1042752-located in the 3'-UTR of POU2AF1, which plays a vital role in lymphomagenesis-was significantly associated with lymphoma risk in a case-control study with 793 patients and 939 controls. Compared with individuals with the rs1042752TT genotype, those with the rs1042752CC genotype had a higher risk of lymphoma (OR = 2.14, 95% CI: 1.55-2.95, P < 0.001), even in stratified analysis for non-Hodgkin lymphoma (OR = 4.58, 95% CI: 2.38-8.81, P < 0.001), B-cell lymphoma (OR = 4.89, 95% CI: 2.46-9.73, P < 0.001), T-cell lymphoma (OR = 4.20, 95% CI: 1.76-10.05, P = 0.001), and Hodgkin lymphoma (OR = 3.62, 95% CI: 1.25-10.46, P = 0.018). Similar results were also observed in a recessive genetic model. Database findings suggested that rs1042752 might affect the interaction of POU2AF1 mRNA with hsa-miR-633. Functional assays confirmed that rs1042752C altered the binding site of hsa-miR-633 and increased POU2AF1 expression in Ramos, HuT 102, and Jurkat E6-1 cell lines. These findings demonstrate for the first time that functional polymorphism in the 3'-UTR of POU2AF1 is associated with susceptibility, and that SNP interaction with hsa-miR-633 affects gene expression and increases the risk of lymphoma.
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Affiliation(s)
- Kan Zhai
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinlong Hu
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, Chinese Academy of Medical Science and Peking Union Medical College, Cancer Institute and Hospital, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, Chinese Academy of Medical Science and Peking Union Medical College, Cancer Institute and Hospital, Beijing, China
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Savio AJ, Bapat B. Modulation of transcription factor binding and epigenetic regulation of the MLH1 CpG island and shore by polymorphism rs1800734 in colorectal cancer. Epigenetics 2017; 12:441-448. [PMID: 28304185 DOI: 10.1080/15592294.2017.1305527] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The MLH1 promoter polymorphism rs1800734 is associated with MLH1 CpG island hypermethylation and expression loss in colorectal cancer (CRC). Conversely, variant rs1800734 is associated with MLH1 shore, but not island, hypomethylation in peripheral blood mononuclear cell DNA. To explore these distinct patterns, MLH1 CpG island and shore methylation was assessed in CRC cell lines stratified by rs1800734 genotype. Cell lines containing the variant A allele demonstrated MLH1 shore hypomethylation compared to wild type (GG). There was significant enrichment of transcription factor AP4 at the MLH1 promoter in GG and GA cell lines, but not the AA cell line, by chromatin immunoprecipitation studies. Preferential binding to the G allele was confirmed by sequencing in the GA cell line. The enhancer-associated histone modification H3K4me1 was enriched at the MLH1 shore; however, H3K27ac was not, indicating the shore is an inactive enhancer. These results demonstrate the role of variant rs1800734 in altering transcription factor binding as well as epigenetics at regions beyond the MLH1 CpG island in which it is located.
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Affiliation(s)
- Andrea J Savio
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada
| | - Bharati Bapat
- a Lunenfeld-Tanenbaum Research Institute, Sinai Health System , Toronto , Ontario , Canada.,b Department of Laboratory Medicine and Pathobiology , University of Toronto , Toronto , Ontario , Canada.,c Department of Pathology , University Health Network , Toronto , Ontario , Canada
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20
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Savio AJ, Mrkonjic M, Lemire M, Gallinger S, Knight JA, Bapat B. The dynamic DNA methylation landscape of the mutL homolog 1 shore is altered by MLH1-93G>A polymorphism in normal tissues and colorectal cancer. Clin Epigenetics 2017; 9:26. [PMID: 28293327 PMCID: PMC5345264 DOI: 10.1186/s13148-017-0326-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/02/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Colorectal cancers (CRCs) undergo distinct genetic and epigenetic alterations. Expression of mutL homolog 1 (MLH1), a mismatch repair gene that corrects DNA replication errors, is lost in up to 15% of sporadic tumours due to mutation or, more commonly, due to DNA methylation of its promoter CpG island. A single nucleotide polymorphism (SNP) in the CpG island of MLH1 (MLH1-93G>A or rs1800734) is associated with CpG island hypermethylation and decreased MLH1 expression in CRC tumours. Further, in peripheral blood mononuclear cell (PBMC) DNA of both CRC cases and non-cancer controls, the variant allele of rs1800734 is associated with hypomethylation at the MLH1 shore, a region upstream of its CpG island that is less dense in CpG sites. RESULTS To determine whether this genotype-epigenotype association is present in other tissue types, including colorectal tumours, we assessed DNA methylation in matched normal colorectal tissue, tumour, and PBMC DNA from 349 population-based CRC cases recruited from the Ontario Familial Colorectal Cancer Registry. Using the semi-quantitative real-time PCR-based MethyLight assay, MLH1 shore methylation was significantly higher in tumour tissue than normal colon or PBMCs (P < 0.01). When shore methylation levels were stratified by SNP genotype, normal colorectal DNA and PBMC DNA were significantly hypomethylated in association with variant SNP genotype (P < 0.05). However, this association was lost in tumour DNA. Among distinct stages of CRC, metastatic stage IV CRC tumours incurred significant hypomethylation compared to stage I-III cases, irrespective of genotype status. Shore methylation of MLH1 was not associated with MSI status or promoter CpG island hypermethylation, regardless of genotype. To confirm these results, bisulfite sequencing was performed in matched tumour and normal colorectal specimens from six CRC cases, including two cases per genotype (wildtype, heterozygous, and homozygous variant). Bisulfite sequencing results corroborated the methylation patterns found by MethyLight, with significant hypomethylation in normal colorectal tissue of variant SNP allele carriers. CONCLUSIONS These results indicate that the normal tissue types tested (colorectum and PBMC) experience dynamic genotype-associated epigenetic alterations at the MLH1 shore, whereas tumour DNA incurs aberrant hypermethylation compared to normal DNA.
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Affiliation(s)
- Andrea J. Savio
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
| | - Miralem Mrkonjic
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3 Canada
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
- Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3 Canada
- Ontario Familial Colorectal Cancer Registry, Cancer Care Ontario, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Surgery, University Health Network, 200 Elizabeth St., Toronto, ON M5G 2C4 Canada
| | - Julia A. Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Dalla Lana School of Public Health, University of Toronto, 155 College St., Toronto, ON M5T 3M7 Canada
| | - Bharat Bapat
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, 60 Murray St., Toronto, Ontario M5T 3L9 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 27 King’s College Circle, Toronto, Ontario M5S 1A1 Canada
- Department of Pathology, University Health Network, 200 Elizabeth St., Toronto, ON M5G 2C4 Canada
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21
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Arriba M, García JL, Rueda D, Pérez J, Brandariz L, Nutu OA, Alonso L, Rodríguez Y, Urioste M, González-Sarmiento R, Perea J. Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes. Neoplasia 2016; 19:28-34. [PMID: 27987438 PMCID: PMC5166699 DOI: 10.1016/j.neo.2016.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023] Open
Abstract
AIM To investigate whether chromosomal instability (CIN) is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability) and CIMP (CpG island methylator phenotype) in early-onset colorectal cancer (EOCRC). METHODS Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis) were analyzed by array comparative genomic hybridization (aCGH), in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs) and the MSI/CIMP condition in EOCRC. RESULTS Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B) and four secondary clusters (A1, A2, B3, B4). The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC), which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected particular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.
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Affiliation(s)
- María Arriba
- Centre for Biomedical Research of the 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Juan L García
- Biomedical Research Institute of Salamanca (IBSAL). University Hospital of Salamanca-USAL-CSIC, P° de San Vicente, 58-182, 37007, Salamanca, Spain; Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Daniel Rueda
- Molecular Biology Laboratory, 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Jessica Pérez
- Biomedical Research Institute of Salamanca (IBSAL). University Hospital of Salamanca-USAL-CSIC, P° de San Vicente, 58-182, 37007, Salamanca, Spain; Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Lorena Brandariz
- Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Oana A Nutu
- Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Laura Alonso
- Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Yolanda Rodríguez
- Department of Pathology, 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Human Cancer Genetics Program. Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro, 3, 28029, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Institute of Health Carlos III, C/Monforte de Lemos 3-5, Pabellón 11, 28029, Madrid, Spain
| | - Rogelio González-Sarmiento
- Biomedical Research Institute of Salamanca (IBSAL). University Hospital of Salamanca-USAL-CSIC, P° de San Vicente, 58-182, 37007, Salamanca, Spain; Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-CSIC, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Perea
- Centre for Biomedical Research of the 12 de Octubre University Hospital, Avda. de Córdoba, S/N, 28041, Madrid, Spain; Department of Surgery, 12 de Octubre University Hospital. Avda. de Córdoba, S/N, 28041, Madrid, Spain.
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22
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Corradin O, Cohen AJ, Luppino JM, Bayles IM, Schumacher FR, Scacheri PC. Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nat Genet 2016; 48:1313-1320. [PMID: 27643537 PMCID: PMC5083135 DOI: 10.1038/ng.3674] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022]
Abstract
SNPs associated with disease susceptibility often reside in enhancer clusters, or super-enhancers. Constituents of these enhancer clusters cooperate to regulate target genes and often extend beyond the linkage disequilibrium (LD) blocks containing risk SNPs identified in genome-wide association studies (GWAS). We identified 'outside variants', defined as SNPs in weak LD with GWAS risk SNPs that physically interact with risk SNPs as part of a target gene's regulatory circuitry. These outside variants further explain variation in target gene expression beyond that explained by GWAS-associated SNPs. Additionally, the clinical risk associated with GWAS SNPs is considerably modified by the genotype of outside variants. Collectively, these findings suggest a potential model in which outside variants and GWAS SNPs that physically interact in 3D chromatin collude to influence target transcript levels as well as clinical risk. This model offers an additional hypothesis for the source of missing heritability for complex traits.
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Affiliation(s)
- Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Andrea J Cohen
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer M Luppino
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ian M Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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23
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Du M, Jiao S, Bien SA, Gala M, Abecasis G, Bezieau S, Brenner H, Butterbach K, Caan BJ, Carlson CS, Casey G, Chang-Claude J, Conti DV, Curtis KR, Duggan D, Gallinger S, Haile RW, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hudson TJ, Jenkins MA, Küry S, Le Marchand L, Leal SM, Newcomb PA, Nickerson DA, Potter JD, Schoen RE, Schumacher FR, Seminara D, Slattery ML, Hsu L, Chan AT, White E, Berndt SI, Peters U. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PLoS One 2016; 11:e0157521. [PMID: 27379672 PMCID: PMC4933364 DOI: 10.1371/journal.pone.0157521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 06/01/2016] [Indexed: 01/27/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).
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Affiliation(s)
- Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Stephanie A. Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States of America
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J. Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, United States of America
| | - Christopher S. Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Graham Casey
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David V. Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Keith R. Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Steven Gallinger
- Department of Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - Robert W. Haile
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, United States of America
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L. Hopper
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark A. Jenkins
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States of America
| | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Deborah A. Nickerson
- Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Fredrick R. Schumacher
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, United States of America
| | - Martha L. Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, United States of America
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
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24
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Identification of a Potential Regulatory Variant for Colorectal Cancer Risk Mapping to 3p21.31 in Chinese Population. Sci Rep 2016; 6:25194. [PMID: 27120998 PMCID: PMC4848543 DOI: 10.1038/srep25194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/12/2016] [Indexed: 01/30/2023] Open
Abstract
Genome-wide association studies (GWAS) have established chromosome 3p21.31 as a susceptibility locus for colorectal cancer (CRC) that lacks replication and exploration in the Chinese population. We searched potentially functional single nucleotide polymorphisms (SNPs) in the linkage disequilibrium (LD) block of 3p21.31 with chromatin immunoprecipitation-sequencing (ChIP-seq) data of histone modification, and tested their association with CRC via a case-control study involving 767 cases and 1397 controls in stage 1 and 528 cases and 678 controls in stage 2. In addition to the tag SNP rs8180040 (odds ratio (OR) = 0.875, 95% confidence interval (95% CI) = 0.793−0.966, P = 0.008, P-FDR (false discovery rate) = 0.040), rs1076394 presented consistently significant associations with CRC risk at both stages with OR = 0.850 (95% CI = 0.771−0.938, P = 0.001, P-FDR = 0.005) under the additive model in combined analyses. Supported by the analyses of data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), it was suggested that rs1076394 served as an expression Quantitative Trait Loci (eQTL) for gene CCDC12 and NME6, while NME6’s expression was obviously higher in CRC tissues. Using biofeature information such as ChIP-seq and RNA sequencing (RNA-seq) data might help researchers to interpret GWAS results and locate functional variants for diseases in the post-GWAS era.
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25
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Salomon MP, Li WLS, Edlund CK, Morrison J, Fortini BK, Win AK, Conti DV, Thomas DC, Duggan D, Buchanan DD, Jenkins MA, Hopper JL, Gallinger S, Le Marchand L, Newcomb PA, Casey G, Marjoram P. GWASeq: targeted re-sequencing follow up to GWAS. BMC Genomics 2016; 17:176. [PMID: 26940994 PMCID: PMC4776370 DOI: 10.1186/s12864-016-2459-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For the last decade the conceptual framework of the Genome-Wide Association Study (GWAS) has dominated the investigation of human disease and other complex traits. While GWAS have been successful in identifying a large number of variants associated with various phenotypes, the overall amount of heritability explained by these variants remains small. This raises the question of how best to follow up on a GWAS, localize causal variants accounting for GWAS hits, and as a consequence explain more of the so-called "missing" heritability. Advances in high throughput sequencing technologies now allow for the efficient and cost-effective collection of vast amounts of fine-scale genomic data to complement GWAS. RESULTS We investigate these issues using a colon cancer dataset. After QC, our data consisted of 1993 cases, 899 controls. Using marginal tests of associations, we identify 10 variants distributed among six targeted regions that are significantly associated with colorectal cancer, with eight of the variants being novel to this study. Additionally, we perform so-called 'SNP-set' tests of association and identify two sets of variants that implicate both common and rare variants in the etiology of colorectal cancer. CONCLUSIONS Here we present a large-scale targeted re-sequencing resource focusing on genomic regions implicated in colorectal cancer susceptibility previously identified in several GWAS, which aims to 1) provide fine-scale targeted sequencing data for fine-mapping and 2) provide data resources to address methodological questions regarding the design of sequencing-based follow-up studies to GWAS. Additionally, we show that this strategy successfully identifies novel variants associated with colorectal cancer susceptibility and can implicate both common and rare variants.
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Affiliation(s)
- Matthew P Salomon
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA. .,Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.
| | - Wai Lok Sibon Li
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - John Morrison
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Barbara K Fortini
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Duncan C Thomas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia. .,Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
| | | | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Paul Marjoram
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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26
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Abstract
Colorectal cancer (CRC) is a complex disease that develops as a consequence of both genetic and environmental risk factors. A small proportion (3-5%) of cases arise from hereditary syndromes predisposing to early onset CRC as a result of mutations in over a dozen well defined genes. In contrast, CRC is predominantly a late onset 'sporadic' disease, developing in individuals with no obvious hereditary syndrome. In recent years, genome wide association studies have discovered that over 40 genetic regions are associated with weak effects on sporadic CRC, and it has been estimated that increasingly large genome wide scans will identify many additional novel genetic regions. Subsequent experimental validations have identified the causally related variant(s) in a limited number of these genetic regions. Further biological insight could be obtained through ethnically diverse study populations, larger genetic sequencing studies and development of higher throughput functional experiments. Along with inherited variation, integration of the tumour genome may shed light on the carcinogenic processes in CRC. In addition to summarising the genetic architecture of CRC, this review discusses genetic factors that modify environmental predictors of CRC, as well as examples of how genetic insight has improved clinical surveillance, prevention and treatment strategies. In summary, substantial progress has been made in uncovering the genetic architecture of CRC, and continued research efforts are expected to identify additional genetic risk factors that further our biological understanding of this disease. Subsequently these new insights will lead to improved treatment and prevention of colorectal cancer.
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Affiliation(s)
- Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
| | - Stephanie Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Niha Zubair
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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27
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Ke J, Lou J, Chen X, Li J, Liu C, Gong Y, Yang Y, Zhu Y, Zhang Y, Gong J. Identification of a Potential Regulatory Variant for Colorectal Cancer Risk Mapping to Chromosome 5q31.1: A Post-GWAS Study. PLoS One 2015; 10:e0138478. [PMID: 26381143 PMCID: PMC4575091 DOI: 10.1371/journal.pone.0138478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/29/2015] [Indexed: 02/07/2023] Open
Abstract
Large-scale genome-wide association studies (GWAS) have established chromosome 5q31.1 as a susceptibility locus for colorectal cancer (CRC), which was still lack of causal genetic variants. We searched potentially regulatory single nucleotide polymorphisms (SNPs) in the overlap region between linkage disequilibrium (LD) block of 5q31.1 and regulatory elements predicted by histone modifications, then tested their association with CRC via a case-control study. Among three candidate common variants, we found rs17716310 conferred significantly (heterozygous model: OR = 1.273, 95% confidence interval (95%CI) = 1.016–1.595, P = 0.036) and marginally (dominant model: OR = 1.238, 95%CI = 1.000–1.532, P = 0.050) increase risk for CRC in a Chinese population including 695 cases and 709 controls. This variation was suggested to be regulatory altering the activity of enhancer that control PITX1 expression. Using epigenetic information such as chromatin immunoprecipitation-sequencing (ChIP-seq) data might help researchers to interpret the results of GWAS and locate causal variants for diseases in post-GWAS era.
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Affiliation(s)
- Juntao Ke
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xueqin Chen
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Liu
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yajie Gong
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Zhang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Gong
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), and Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail:
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28
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Hulur I, Gamazon ER, Skol AD, Xicola RM, Llor X, Onel K, Ellis NA, Kupfer SS. Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci. BMC Genomics 2015; 16:138. [PMID: 25766683 PMCID: PMC4351699 DOI: 10.1186/s12864-015-1292-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/29/2015] [Indexed: 12/20/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases. Results 8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn’s disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2). Enrichment of colon eQTL near transcription start sites and for active histone marks was demonstrated, and eQTL with high population differentiation were identified. Conclusions Through the comprehensive study of eQTL in the human colon, this study identified novel target genes for IBD- and CRC-associated genetic variants. Moreover, bioinformatic characterization of colon eQTL provides a tissue-specific tool to improve understanding of biological differences in diseases between different ethnic groups. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1292-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imge Hulur
- Committee on Genetics, Genomics and Systems Biology, Chicago, IL, 60637, USA.
| | - Eric R Gamazon
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA. .,Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, 37232, USA.
| | - Andrew D Skol
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
| | - Rosa M Xicola
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Xavier Llor
- Department of Medicine, Yale University, New Haven, CT, 06510, USA.
| | - Kenan Onel
- Department of Pediatrics, University of Chicago, Chicago, IL, 60637, USA.
| | - Nathan A Ellis
- University of Arizona Cancer Center, Tucson, AZ, 85724, USA.
| | - Sonia S Kupfer
- Department of Medicine, 900 East 57th Street, MB#9, Chicago, IL, 60637, USA.
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29
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Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A, Whiffin N, Carnicer MJ, Broome L, Dryden N, Nagano T, Schoenfelder S, Enge M, Yuan Y, Taipale J, Fraser P, Fletcher O, Houlston RS. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun 2015; 6:6178. [PMID: 25695508 PMCID: PMC4346635 DOI: 10.1038/ncomms7178] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 12/30/2014] [Indexed: 12/25/2022] Open
Abstract
Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.
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Affiliation(s)
- Roland Jäger
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Gabriele Migliorini
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Radhika Kandaswamy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Helen E. Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Andreas Heindl
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Maria J. Carnicer
- Division of Molecular Pathology, Haemato-Oncology Research Unit, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Laura Broome
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Nicola Dryden
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Martin Enge
- Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, 14 183, Huddinge, Sweden
| | - Yinyin Yuan
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Science for Life Laboratory, Karolinska Institutet, 14 183, Huddinge, Sweden
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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30
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Fortini BK, Tring S, Plummer SJ, Edlund CK, Moreno V, Bresalier RS, Barry EL, Church TR, Figueiredo JC, Casey G. Multiple functional risk variants in a SMAD7 enhancer implicate a colorectal cancer risk haplotype. PLoS One 2014; 9:e111914. [PMID: 25375357 PMCID: PMC4223076 DOI: 10.1371/journal.pone.0111914] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/01/2014] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWAS) of colorectal cancer (CRC) have led to the identification of a number of common variants associated with modest risk. Several risk variants map within the vicinity of TGFβ/BMP signaling pathway genes, including rs4939827 within an intron of SMAD7 at 18q21.1. A previous study implicated a novel SNP (novel 1 or rs58920878) as a functional variant within an enhancer element in SMAD7 intron 4. In this study, we show that four SNPs including novel 1 (rs6507874, rs6507875, rs8085824, and rs58920878) in linkage disequilibrium (LD) with the index SNP rs4939827 demonstrate allele-specific enhancer effects in a large, multi-component enhancer of SMAD7. All four SNPs demonstrate allele-specific protein binding to nuclear extracts of CRC cell lines. Furthermore, some of the risk-associated alleles correlate with increased expression of SMAD7 in normal colon tissues. Finally, we show that the enhancer is responsive to BMP4 stimulation. Taken together, we propose that the associated CRC risk at 18q21.1 is due to four functional variants that regulate SMAD7 expression and potentially perturb a BMP negative feedback loop in TGFβ/BMP signaling pathways.
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Affiliation(s)
- Barbara K. Fortini
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
| | - Stephanie Tring
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Sarah J. Plummer
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Christopher K. Edlund
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology, CIBERESP and University of Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - Robert S. Bresalier
- Department of Gastroenterology, Hepatology and Nutrition, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Elizabeth L. Barry
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Timothy R. Church
- Division of Environmental Health Sciences, University of Minnesota School of Public Health, Minneapolis, Minnesota, United States of America
| | - Jane C. Figueiredo
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
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31
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Closa A, Cordero D, Sanz-Pamplona R, Solé X, Crous-Bou M, Paré-Brunet L, Berenguer A, Guino E, Lopez-Doriga A, Guardiola J, Biondo S, Salazar R, Moreno V. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. Carcinogenesis 2014; 35:2039-46. [PMID: 24760461 DOI: 10.1093/carcin/bgu092] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this study, we aim to identify the genes responsible for colorectal cancer risk behind the loci identified in genome-wide association studies (GWAS). These genes may be candidate targets for developing new strategies for prevention or therapy. We analyzed the association of genotypes for 26 GWAS single nucleotide polymorphisms (SNPs) with the expression of genes within a 2 Mb region (cis-eQTLs). Affymetrix Human Genome U219 expression arrays were used to assess gene expression in two series of samples, one of healthy colonic mucosa (n = 47) and other of normal mucosa adjacent to colon cancer (n = 97, total 144). Paired tumor tissues (n = 97) were also analyzed but did not provide additional findings. Partial Pearson correlation (r), adjusted for sample type, was used for the analysis. We have found Bonferroni-significant cis-eQTLs in three loci: rs3802842 in 11q23.1 associated to C11orf53, COLCA1 (C11orf92) and COLCA2 (C11orf93; r = 0.60); rs7136702 in 12q13.12 associated to DIP2B (r = 0.63) and rs5934683 in Xp22.3 associated to SHROOM2 and GPR143 (r = 0.47). For loci in chromosomes 11 and 12, we have found other SNPs in linkage disequilibrium that are more strongly associated with the expression of the identified genes and are better functional candidates: rs7130173 for 11q23.1 (r = 0.66) and rs61927768 for 12q13.12 (r = 0.86). These SNPs are located in DNA regions that may harbor enhancers or transcription factor binding sites. The analysis of trans-eQTLs has identified additional genes in these loci that may have common regulatory mechanisms as shown by the analysis of protein-protein interaction networks.
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Affiliation(s)
- Adria Closa
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - David Cordero
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Rebeca Sanz-Pamplona
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Xavier Solé
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Marta Crous-Bou
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Laia Paré-Brunet
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Antoni Berenguer
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Elisabet Guino
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Adriana Lopez-Doriga
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Jordi Guardiola
- Gastroenterology Service, Bellvitge University Hospital, Barcelona E08907, Spain and
| | - Sebastiano Biondo
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona E08907, Spain, General and Digestive Surgery Service, Bellvitge University Hospital, Barcelona E08907, Spain
| | - Ramon Salazar
- Medical Oncology Service, Catalan Institute of Oncology, Barcelona E08907, Spain
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain, Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona E08907, Spain,
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Rasool S, Rasool V, Naqvi T, Ganai BA, Shah BA. Genetic unraveling of colorectal cancer. Tumour Biol 2014; 35:5067-82. [PMID: 24573608 DOI: 10.1007/s13277-014-1713-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/29/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is a common disease in both men and women (being the third most common cancer in men and the second most common among women) and thus represents an important and serious public health issue, especially in the western world. Although it is a well-established fact that cancers of the large intestine produce symptoms relatively earlier at a stage that can be easily cured by resection, a large number of people lose their lives to this deadly disease each year. Recent times have seen an important change in the incidence of colorectal cancer in different parts of the world. The etiology of colorectal cancer is multifactorial and is likely to involve the actions of genes at multiple levels along the multistage carcinogenesis process. Exhaustive efforts have been made out in the direction of unraveling the role of various environmental factors, gene mutations, and polymorphisms worldwide (as well as in Kashmir-"a valley of gastrointestinal cancers") that have got a role to play in the development of this disease so that antitumor drugs could be developed against this cancer, first, and, finally, the responsiveness or resistance to these agents could be understood for combating this global issue.
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Affiliation(s)
- Sabha Rasool
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, 190006, Kashmir, India
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